Re: [AMBER] Generating an asymmetric box for Steered MD

From: Souvik Dey <>
Date: Thu, 16 Apr 2020 14:33:36 -0500

Hi David,

What I am concerned about is how AddToBox would work. For example, let's
say that I want to create a box of 120Å x 60Å x 60Å. and fill it with tip3p
water molecules. If I now try to set the box dimensions by setting -X/Y/Z
AddToBox shows that the identifier -X is unknown.

My questions are,
1. How should I set up my box dimensions before I fill it up with the
required number of solvent molecules by -na flag?
2. How would the program understand that the water I add is tip3p since all
I am providing is a PDB file of a single water molecule with the -a flag?

Thank you for your time.

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Received on Thu Apr 16 2020 - 13:00:02 PDT
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